Understanding the determinants of stability and folding of small globular proteins from their energetics

The results of minimal model calculations suggest that the stability and the kinetic accessibility of the native state of small globular proteins are controlled by few "hot" sites. By mean of molecular dynamics simulations around the native conformation, which simulate the protein and the surrounding solvent at full--atom level, we generate an energetic map of the equilibrium state of the protein and simplify it with an Eigenvalue decomposition. The components of the Eigenvector associated with the lowest Eigenvalue indicate which are the "hot" sites responsible for the stability and for the fast folding of the protein. Comparison of these predictions with the results of mutatgenesis experiments, performed for five small proteins, provide an excellent agreement

Correlated Binomial Models and Correlation Structures

We discuss a general method to construct correlated binomial distributions by imposing several consistent relations on the joint probability function. We obtain self-consistency relations for the conditional correlations and conditional probabilities. The beta-binomial distribution is derived by a strong symmetric assumption on the conditional correlations. Our derivation clarifies the 'correlation' structure of the beta-binomial distribution. It is also possible to study the correlation structures of other probability distributions of exchangeable (homogeneous) correlated Bernoulli random variables. We study some distribution functions and discuss their behaviors in terms of their correlation structures.Comment: 12 pages, 7 figure

Influence of conformational fluctuations on enzymatic activity: modelling the functional motion of beta-secretase

Considerable insight into the functional activity of proteins and enzymes can be obtained by studying the low-energy conformational distortions that the biopolymer can sustain. We carry out the characterization of these large scale structural changes for a protein of considerable pharmaceutical interest, the human $\beta$-secretase. Starting from the crystallographic structure of the protein, we use the recently introduced beta-Gaussian model to identify, with negligible computational expenditure, the most significant distortion occurring in thermal equilibrium and the associated time scales. The application of this strategy allows to gain considerable insight into the putative functional movements and, furthermore, helps to identify a handful of key regions in the protein which have an important mechanical influence on the enzymatic activity despite being spatially distant from the active site. The results obtained within the Gaussian model are validated through an extensive comparison against an all-atom Molecular Dynamics simulation.Comment: To be published in a special issue of J. Phys.: Cond. Mat. (Bedlewo Workshop

Poisson-Bracket Approach to the Dynamics of Nematic Liquid Crystals. The Role of Spin Angular Momentum

Nematic liquid crystals are well modeled as a fluid of rigid rods. Starting from this model, we use a Poisson-bracket formalism to derive the equations governing the dynamics of nematic liquid crystals. We treat the spin angular momentum density arising from the rotation of constituent molecules about their centers of mass as an independent field and derive equations for it, the mass density, the momentum density, and the nematic director. Our equations reduce to the original Leslie-Ericksen equations, including the inertial director term that is neglected in the hydrodynamic limit, only when the moment of inertia for angular momentum parallel to the director vanishes and when a dissipative coefficient favoring locking of the angular frequencies of director rotation and spin angular momentum diverges. Our equations reduce to the equations of nematohydrodynamics in the hydrodynamic limit but with dissipative coefficients that depend on the coefficient that must diverge to produce the Leslie-Ericksen equations.Comment: 10 pages, to be published in Phys. Rev. E 72(5

Fifteen years of XMM-Newton and Chandra monitoring of Sgr A*: Evidence for a recent increase in the bright flaring rate

We present a study of the X-ray flaring activity of Sgr A* during all the 150 XMM-Newton and Chandra observations pointed at the Milky Way center over the last 15 years. This includes the latest XMM-Newton and Chandra campaigns devoted to monitoring the closest approach of the very red Br-Gamma emitting object called G2. The entire dataset analysed extends from September 1999 through November 2014. We employed a Bayesian block analysis to investigate any possible variations in the characteristics (frequency, energetics, peak intensity, duration) of the flaring events that Sgr A* has exhibited since their discovery in 2001. We observe that the total bright-or-very bright flare luminosity of Sgr A* increased between 2013-2014 by a factor of 2-3 (~3.5 sigma significance). We also observe an increase (~99.9% significance) from 0.27+-0.04 to 2.5+-1.0 day^-1 of the bright-or-very bright flaring rate of Sgr A*, starting in late summer 2014, which happens to be about six months after G2's peri-center passage. This might indicate that clustering is a general property of bright flares and that it is associated with a stationary noise process producing flares not uniformly distributed in time (similar to what is observed in other quiescent black holes). If so, the variation in flaring properties would be revealed only now because of the increased monitoring frequency. Alternatively, this may be the first sign of an excess accretion activity induced by the close passage of G2. More observations are necessary to distinguish between these two hypotheses.Comment: Accepted for publication in MNRA

A model to explain angular distributions of J/ψJ/\psi and ψ(2S)\psi(2S) decays into ΛΛ‾\Lambda\overline{\Lambda} and Σ0Σ‾0\Sigma^0\overline{\Sigma}^0

BESIII data show a particular angular distribution for the decay of the $J/\psi$ and $\psi(2S)$ mesons into the hyperons $\Lambda\overline{\Lambda}$ and $\Sigma^0\overline{\Sigma}^0$. More in details the angular distribution of the decay $\psi(2S) \to \Sigma^0\overline{\Sigma}^0$ exhibits an opposite trend with respect to that of the other three channels: $J/\psi \to \Lambda\overline{\Lambda}$, $J/\psi \to \Sigma^0\overline{\Sigma}^0$ and $\psi(2S) \to \Lambda\overline{\Lambda}$. We define a model to explain the origin of this phenomenon.Comment: 6 pages, 7 figures, to be published in Chinese Physics

Caracterização e avaliação econômica de sistemas de cultivo de trigo nos Biomas Pampa, Mata Atlântica e Cerrado.

Este capítulo tem por objetivos descrever a evolução da produção de trigo nos biomas Pampa, Mata Atlântica e Cerrado, bem como analisar os sistemas de cultivo do cereal e seus indicadores técnicos em cada um desses biomas e, especificamente, caracterizar tais sistemas sob a perspectiva da viabilidade socioeconômica.bitstream/item/208335/1/CaracterizacaoAvaliacaoEconomica.pd

Temperature dependence of the resistivity in the double-exchange model

The resistivity around the ferromagnetic transition temperature in the double exchange model is studied by the Schwinger boson approach. The spatial spin correlation responsible for scattering of conduction electrons are taken into account by adopting the memory function formalism. Although the correlation shows a peak lower than the transition temperature, the resistivity in the ferromagnetic state monotonically increases with increasing temperature due to a variation of the electronic state of the conduction electron. In the paramagnetic state, the resistivity is dominated by the short range correlation of scattering and is almost independent of the temperature. It is attributed to a cancellation between the nearest-neighbor spin correlation, the fermion bandwidth, and the fermion kinetic energy. This result implies the importance of the temperature dependence of the electronic states of the conduction electron as well as the localized spin states in both ferromagnetic and paramagnetic phases.Comment: RevTex, 4 pages, 4 PostScript figures, To appear in Phys. Rev.